samplot_commands: Prepare Samplot Commands from VCF

In pdiakumis/rock: Rocking R at UMCCR

Description

Prepares Samplot commands from a structural variant VCF and paths to required BAM files.

Usage

samplot_commands(vcf_file, bam_file, sample_nm, out_dir = NULL, other = "")

Arguments

vcf_file	Path to the Manta VCF file (any SV VCF should work, really). Can be compressed or not.
bam_file	Path(s) to BAM file(s) (atomic vector).
sample_nm	Name(s) of BAM file(s) to display in plot (atomic vector).
out_dir	Output directory.
other	Other arguments to pass to Samplot (single string).

Value

A dataframe (tibble) with the following:

• chrom1: CHROM

• pos1: POS | INFO/BPI_START

• chrom2: CHROM (for mate2 if BND)

• pos2: INFO/END | INFO/BPI_END (for mate1 if BND)

• svtype: INFO/SVTYPE

• svlen: 'pos2 - pos2“ if not BND, else 0

• cl: Command line for Samplot

Examples

## Not run: 
vcf_file <- "path/to/vcf1.vcf.gz"
bam_file <- c("bam1", "bam2")
sample_nm <- c("s1", "s2")
samplot_commands(vcf_file, bam_file, sample_nm)

## End(Not run)

pdiakumis/rock documentation built on Oct. 12, 2020, 9:38 a.m.